Harmful R-loops are prevented via different cell cycle-specific mechanisms

Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts

(2021) Kevin S. Lang et al.   Cell Reports

Ultra-Deep Coverage Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

(2020) Maika Malig et al.   JOURNAL OF MOLECULAR BIOLOGY

Negative supercoil at gene boundaries modulates gene topology

(2020) Yathish Jagadheesh Achar et al.   NATURE

Regulatory R-loops as facilitators of gene expression and genome stability

(2020) Christof Niehrs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Sen1 Is Recruited to Replication Forks via Ctf4 and Mrc1 and Promotes Genome Stability

(2020) Rowin Appanah et al.   Cell Reports

UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide

(2020) Carmen Pérez-Calero et al.   GENES & DEVELOPMENT

SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations

(2020) A. Takedachi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

(2020) Alexy Promonet et al.   Nature Communications

Harmful DNA:RNA hybrids are formed in cis and in a Rad51-independent manner

(2020) Juan Lafuente-Barquero et al.   eLife

BRD4 prevents the accumulation of R-loops and protects against transcription–replication collision events and DNA damage

(2020) Fred C. Lam et al.   Nature Communications

Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex

(2020) Sandra K Schuller et al.   eLife

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

R-Loops as Cellular Regulators and Genomic Threats

(2019) Madzia P. Crossley et al.   MOLECULAR CELL

Transcription-mediated replication hindrance: a major driver of genome instability

(2019) Belén Gómez-González et al.   GENES & DEVELOPMENT

Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

(2019) Julieta Rivosecchi et al.   EMBO JOURNAL

The DNA damage response acts as a safeguard against harmful DNA–RNA hybrids of different origins

(2019) Sonia Barroso et al.   EMBO REPORTS

R Loops: From Physiological to Pathological Roles

(2019) Tatiana García-Muse et al.   CELL

Yra1-bound RNA–DNA hybrids cause orientation-independent transcription–replication collisions and telomere instability

(2018) María García-Rubio et al.   GENES & DEVELOPMENT

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast

(2018) Stella R. Hartono et al.   JOURNAL OF MOLECULAR BIOLOGY

Cell-Cycle Modulation of Transcription Termination Factor Sen1

(2018) Hannah E. Mischo et al.   MOLECULAR CELL

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination

(2018) Claudia Ribeiro de Almeida et al.   MOLECULAR CELL

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

(2018) Courtney W. Hanna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations

(2018) Sarah Cohen et al.   Nature Communications

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

(2018) Courtney W. Hanna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented by the RNA:DNA helicase Senataxin

(2018) Julien Brustel et al.   Scientific Reports

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage

(2018) Agnese Cristini et al.   Cell Reports

Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability

(2018) Lorenzo Costantino et al.   MOLECULAR CELL

R‐loop formation during S phase is restricted by PrimPol‐mediated repriming

(2018) Saša Šviković et al.   EMBO JOURNAL

Human mitochondrial degradosome prevents harmful mitochondrial R loops and mitochondrial genome instability

(2018) Sonia Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sae2/CtIP prevents R-loop accumulation in eukaryotic cells

(2018) Nodar Makharashvili et al.   eLife

Genome Instability and γH2AX

(2017) Anastasios Georgoulis et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Senataxin: Genome Guardian at the Interface of Transcription and Neurodegeneration

(2017) Matthias Groh et al.   JOURNAL OF MOLECULAR BIOLOGY

R Loops and Links to Human Disease

(2017) Patricia Richard et al.   JOURNAL OF MOLECULAR BIOLOGY

Histone Mutants Separate R Loop Formation from Genome Instability Induction

(2017) Desiré García-Pichardo et al.   MOLECULAR CELL

DNA–RNA hybrids: the risks of DNA breakage during transcription

(2017) Andrés Aguilera et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription

(2017) Alessandra Brambati et al.   NUCLEIC ACIDS RESEARCH

Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin

(2017) Aleix Bayona-Feliu et al.   Nature Communications

DNA–RNA hybrids: the risks of DNA breakage during transcription

(2017) Andrés Aguilera et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces cerevisiaeSen1 Helicase Domain Exhibits 5′- to 3′-Helicase Activity with a Preference for Translocation on DNA Rather than RNA

(2015) Stephen Martin-Tumasz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair

(2015) Elodie Hatchi et al.   MOLECULAR CELL

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae

(2014) Ignacio Soriano et al.   BMC GENOMICS

The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts

(2014) E. Herrera-Moyano et al.   GENES & DEVELOPMENT

Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability

(2014) Julie Sollier et al.   MOLECULAR CELL

R-loops Associated with Triplet Repeat Expansions Promote Gene Silencing in Friedreich Ataxia and Fragile X Syndrome

(2014) Matthias Groh et al.   PLoS Genetics

Senataxin Associates with Replication Forks to Protect Fork Integrity across RNA-Polymerase-II-Transcribed Genes

(2012) Amaya Alzu et al.   CELL

Architecture and nucleic acids recognition mechanism of the THO complex, an mRNP assembly factor

(2012) Álvaro Peña et al.   EMBO JOURNAL

Senataxin, Defective in the Neurodegenerative Disorder Ataxia with Oculomotor Apraxia 2, Lies at the Interface of Transcription and the DNA Damage Response

(2012) O. Yuce et al.   MOLECULAR AND CELLULAR BIOLOGY

Depleting Components of the THO Complex Causes Increased Telomere Length by Reducing the Expression of the Telomere-Associated Protein Rif1p

(2012) Tai-Yuan Yu et al.   PLoS One

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles

(2011) Belén Gómez-González et al.   EMBO JOURNAL

R-loop-mediated genomic instability is caused by impairment of replication fork progression

(2011) W. Gan et al.   GENES & DEVELOPMENT

Yeast Sen1 Helicase Protects the Genome from Transcription-Associated Instability

(2011) Hannah E. Mischo et al.   MOLECULAR CELL

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

(2011) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing

(2011) N. Jamonnak et al.   RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation

(2009) Amila Suraweera et al.   HUMAN MOLECULAR GENETICS

Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription

(2009) Sandie Tuduri et al.   NATURE CELL BIOLOGY

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS